Mass Effect 1. New Beginnings

**Completion**

**Chapter One: New Beginnings**

"I was expecting something like this," Chakwas says. She looks down into her mug, swishes the brown liquid, and downs it in one gulp. "I'm just surprised it wasn't sooner." She gestures at the seat in front of her.

"The mission kept her going," the yeoman says, slipping into the offered chair. "As long as she had people depending on her, she could ignore everything else. Dying, Cerberus, and don't forget about Kaidan. It was years ago for us, but it's only been a few weeks for her."

"It's so easy to forget that she's human too."

"Well, mostly human," Kelly says, and Chakwas glances over at the woman – _hero, saviour, champion. But, after all that, just a woman_ – lying on the bed behind her.

"Human in all the places it matters," Chakwas says, then sighs. "You're right, she's had a lot riding on her shoulders and we've, well we've just stepped back and let her carry it all." They sit in silence for a moment, then Chakwas replaces the mug on the table with a clink. "Still," she says, "I didn't expect her reaction to be so… severe."

"It's classic post-traumatic stress disorder, if that helps."

"She didn't recognise who I was, Kelly. She turned her gun on me, called me a Cerberus traitor, and demanded to know where the control chip was. I don't know what would have happened if Miranda hadn't…"

"She dealt with the situation." Kelly's voice is deliberately calming, and it angers Chakwas. She forces the emotion down, swallows.

"I know, and I'm grateful, but I don't know how long we can keep her sedated like this. We need a plan."

"Well," the yeoman says, and rubs the back of her neck with one hand, "I've looked into her files… Her psychological profile, to be specific."

"Aren't those Alliance classified?"

"Miranda authorised it," says Kelly, ignoring Chakwas' astonished look. "But that's beside the point. Shepard thrives in high pressure situations. It's one of her great strengths. It's how she pulled everyone together during the Skyllian Blitz, and it could help her again now."

"She can't be in high pressure situations forever. Even Shepard needs some down time."

"Yes, but Shepard doesn't exactly seem the counselling type. She needs a way to process everything that has happened using her strengths. We can help her with that."

"How?"

"I've thought about this. If we reconstruct some of her past missions, ask EDI to code in her past companions, it might give her a chance to come to terms with what's happened. We could patch her implants into the simulation system. For her, it would seem as real as life."

"Isn't that cruel? Making her relive everything that traumatised her? Do I need to remind you that she hasn't consented to this?"

"This could help her to come to terms with what has happened, allow her to work through the trauma. She either does it on her own, or with our help."

Chakwas stares at the red-headed woman, whose gaze is not flinching. Behind her, she can feel the presence of the Commander – her strength of will formidable even when unconscious. And, like an oily snake within, she can feel the lingering terror of this morning's episode. The moment when she was staring down the barrel of her Captain's gun.

_If it would help_, she thinks. But she's being selfish, and she knows it. She wants the real Shepard back. Not this… this… _crazy person_.

Did she really think that? She knows all about post-traumatic stress disorder, she's seen it happen to far too many soldiers. Why is this one hitting her so hard?

Too much too soon. She puts it away to analyse… later.

"I would insist on being present to monitor her condition," Chakwas says, and Kelly nods as though she is expecting it. The doctor's eyes narrow.

"You've already asked Miranda, haven't you?" Chakwas says mildly.

"She's the one who ordered it, Doctor. That's why I came to speak with you."

* * *

Shepard wakes.

She's in bed, and a warm familiar body is lying next to her, one arm thrown over her waist.

For a moment she is confused, then she turns her head to see:

"Kaidan!"

_Why is she so relieved to see him?_

He stirs at the sound of his name, opens his eyes. "Morning, sunshine," he says, and stretches. "Up and at 'em, I guess. Big day today."

Then she remembers. Today is Virmire; to meet with the Salarian reconnaissance team.

She's out of bed, dressing swiftly, and reaches for the data pad on her desk, flicking to the details of the mission.

Kaidan sits up in bed, the sheet draped around his toned midsection. His hair is sticking up at odd angles, but she doesn't spare a glance.

"Have I ever told you that I love watching you work?" he says with a smile, "Because it's a lucky thing I do."

"This mission could be dangerous," she says, not looking up from the pad. A frown creases her brow and she leans forward on the desk, studying the topography of the planet. "There's plenty of places for ambushes. They could be pinned down when we arrive."

"What makes you think that?" Kaidan asks, standing up and stretching again. The sheet falls away, and he does nothing to hide what it reveals.

"I don't know," she says, glances over, then rubs her forehead with one hand. "Gut feeling, I guess."

"That's what makes you a great Commander." He finds his pants, pulls them, and runs a hand through his short black hair. "I'd better report to the Mess, or people will start talking." He pulls on his shirt, crosses the room, and kisses her cheek. Shepard lowers the datapad and smiles at him.

"See you soon, soldier," she says, and he smiles, snaps her a salute, and leaves her quarters.

* * *

"Vitals good, steady," says Chakwas. "Is she in the simulation now?"

Kelly is hunched over on her chair, looking at a graph that has calm, steady waves. "She's in," she says, "Brain function normal."

"What is she seeing?" the Doctor asks.

"She has control over that. The computer will comply with whatever her subconscious desires."

"Is there any way that we can see what she's seeing?"

"There is," says Kelly, and fiddles with the controls on the desk. "… There." An image flickers up onto the screen. A datapad, the topography of Virmire on it.

"Virmire," says Chakwas. "I should have known."

"That's where she lost Lieutenant Alenko, wasn't it?"

"The very same."

"It was a brave decision."

"It was the only decision she could have made. She… well, you already know she had feelings for Alenko."

"But wouldn't that have skewed her towards him?"

"Exactly. And she would never let her judgement be compromised by her emotions."

"So she chose Williams."

Chakwas looks over the monitors at the fresh-faced yeoman. _Young. Unscarred. She's never had to make a decision like the one Shepard faced._

The Doctor nods. "She chose Williams," she agrees. _And I hope you never have to face the same kind of choice._

* * *

"I'm sorry, Kaidan."

It's her voice speaking, but it sounds like a stranger's.

_What am I doing? Kaidan, no, no, no…_

"I understand, Commander." And in those words she can hear his love, his resignation, his fear.

_No, no, no… Not again!_

And time…

freezes…

rewinds…

"What the hell are you doing, Williams?" She barks into the mike, her voice angry.

"Making sure this bomb goes off. No matter what. Now go get the lieutenant, and get out of here!"

She's standing on the walkway with Garrus and Tali. One corridor leads back to Kaidan, the other to Williams. The sounds of combat flow through her headset.

"Belay that. We can handle ourselves. Go back and get Williams." Kaidan's voice comes over her headset, breathing hard. _He's alive_. A flood of relief. And she knows that she can't, she just _can't_ leave him to die. _Not again._

A moment.

A decision.

Then –

"Alenko, radio Joker and tell him to meet us on the AA tower."

Kaidan's voice. Reluctant, but understanding. "Yes, Commander. I-''

"You know it's the right choice, L.T," says Williams. And she is being brave, so brave. It breaks her heart.

"I'm sorry," is all she can say. And it doesn't seem nearly enough.

* * *

"Wait," says Kelly. "That's not how it happened."

She's looking at a readout, her eyebrows pulled together. "She was meant to relive it, not reinvent it."

"You said she was the one in control," says Chakwas, amusement barely concealed. _Just like Shepard to turn the tables, even when she's sedated and unconscious._ "Maybe this is what she really needs."

"Maybe we should just pull her out," says Kelly, "This was a bad idea."

"You started this," Chakwas points out. "I say we let it run its course."

"But I don't know what this will do, Doctor."

"So let's find out."

* * *

"I can't believe we just left her down there," says Kaidan. He's sitting on the edge of her bed, she's facing him from her chair.

"There was no time," She spreads her hands out, a disarming gesture: _Please forgive me_. "I couldn't save you both."

"But why me? Why not her?" His face is contorted, pain barely concealed behind lips tight against teeth.

"I'm sorry, Kaidan. I'd never leave you behind. I couldn't. You know that."

"I know, and I am grateful. But Ash died because of me, because of _us_." His brown eyes are molten liquid, and she's looks away to avoid his gaze.

"I know," she says, quietly. There is no getting around it. _He's right._ She put her feelings, and their relationship, ahead of all other concerns. Ahead of Ashley. She looks back up at Kaidan, and he's shaking his head, not looking at her.

"I might- I might need some time," he says, stands. He's still avoiding her eyes.

She nods, looks up at him. "So do I," she says, but she isn't sure if she's lying.

"We'll talk later, Shepard."

"Later," she agrees.

When he leaves, she realises that she'll be alone tonight. Without him, her quarters are a cold and sterile place. Strange how she hadn't noticed that before.

But there is paperwork calling her name. And no time to think.

**END CHAPTER 1**

* * *

**Author's Note:** This is the first chapter of a brand new fic I'm working out. Due to the subject matter, this is a bit AU, and it might be a little OOC but I've tried to keep it in-character as much as possible. Comments and constructive criticism welcome, please read and review! :D


	2. Broken Hearts

**Chapter 2: Broken Hearts**

"So, what are you going to do now?" He's leaning against her doorframe, watching as she fills in the last of the paperwork. He hasn't spoken privately to her since Virmire, and she's surprised he's here now. "Are you taking any shore leave?"

"I didn't have plans to," she says, signing her name with a flourish. _Done_. She looks up, "What about you?"

"There are a few places I want to go. Back to Earth, mostly. There's a small holiday island I want to visit: Hawai'i."

"I've never spent much time on Earth," she says, "I was space-born."

"You'd like it," Kaidan says. "It's all white sand, palm trees, and waves. Or at least that's what the brochure looks like." He pauses, and she says nothing, letting the silence stretch out.

"Maybe you should come," he says. "You know, if you can tear yourself away from your paperwork."

She searches his face, sees hope, perhaps a touch of concern. Is it still too raw? _No, _she decides. She puts her pen down. Stands. Walks over to him, close, but not touching. He doesn't pull back.

"That sounds like a very good idea," she says.

* * *

"What happened to Ilos? To the battle with Saren?"

"Presumably she's at peace with them," Chakwas says, noticing a small spike in blood pressure. "She doesn't need to relive everything." She looks up at the display, "Where are we now?"

"The Normandy, right before the Collector attack," says Miranda, and Chakwas looks up to see her walk through the door of the med clinic. The XO catches Chakwas' glance, meets her gaze, then turns to Kelly. "I came to see how our patient is doing."

"She's doing fine," says Kelly, "But there may have been a slight… miscalculation."

"Miscalculation?" Miranda's blue eyes flash with anger, and Kelly almost squeaks in her haste to repair the damage.

"Nothing major, just a slight… adjustment to how we thought things would happen."

Miranda's eyes meet the Doctor's. Demanding an explanation.

"Shepard is in the simulation, and she's doing fine, but she's not reliving the past," the Doctor says with as much gravity as she can muster, "She's rewriting it."

"What do you mean? What is she rewriting?"

"In the timeline she is experiencing, Lieutenant Alenko is still alive."

Miranda stalks over, turns the monitor towards her. "So I see." She turns to the yeoman, "I want an explanation, Chambers. What does this mean?"

"I don't know." Kelly sounds miserable.

"I don't want her to wake up and fall apart again," says Miranda. "This was supposed to fix her, not give her more issues." She looks at the yeoman, who seems to shrink in the chair. "Find a way to sort it. Now." And whatever Kelly is about to say is cut off as Miranda stalks out of the room.

Kelly looks up at Chakwas, but the Doctor doesn't meet her gaze.

* * *

"That's an order, Alenko!" The ship is burning around them, but still he hesitates, looking between her and the corridor leading to the escape pods. "For god's sake, go!"

Finally, he does, and Shepard turns back to the corridor. It is filled with smoke and fire, but her suit deflects the burning debris as she runs towards the cockpit.

She can hear Joker's voice through her helmet; panicked, angry, afraid.

"Mayday, mayday! We have suffered heavy damage from an unknown enemy!"

As she steps through the doorway to the CIC, the air rushes out of the corridor and into empty space. Her suit's magnetic boots switch on, and she watches as the fire and debris disappear towards the planet looming through the shattered hull overhead.

And there is… silence.

Her breathing is loud, laboured, inside her helmet.

One foot in front of the other. The magnetic boots slow her down, but she has to get to Joker.

_Even if it costs your life?_

The thought comes from nowhere. She shoves it aside. Pushes on. Past the chairs of the navigators, floating in space. Through the barrier sealing off the cockpit.

Joker is, of course, still in his chair. And being a royal dick about it.

"I'm not leaving," he says, his eyes fixed on the Normandy's diagnostics as his hands fly over the display. "I can still save her."

"Joker, she's lost. And you are _not_ going down with the ship." She physically hauls him out of his chair, throws him over her shoulder.

"Hey!" he cries, but it is too late. She shoves him inside the escape pod, steps back to hit the release. "Wait, aren't you coming?" But she knows she won't be. She hits the button to eject the shuttle, and lets the explosion propel her into space.

_Again._

* * *

Silence falls over the med bay as Kelly and Chakwas watch Shepard's final moments.

"I… I had no idea it was so painful," the yeoman says, and swallows heavily.

"She knew it was coming." Chakwas says, her voice filled with wonder. "She accepted it."

"Why would she do that? She changed the past, saved Kaidan… Why didn't she save herself?"

"I don't know," says Chakwas. "Maybe this was something she felt she did right."

"Dying?"

"Saving Joker."

* * *

Shepard wakes. Again. There is no warm body lying beside her this time, just cold blue eyes looking down at her. She tries to move, but can't. The woman gestures to someone out of sight. A rush of fluid in her veins.

Oblivion.

* * *

Shepard looks down at the dossier, wondering how in space she ended up working for Cerberus. Miranda is hovering nearby, but Shepard does her best to ignore her. _I guess being brought back from the dead makes you mighty grateful_, she thinks and that's the only reason she has. That, and the Council's stubborn refusal to believe any of her reports about the Reapers. _At least Cerberus believes me_. But maybe that's not good enough.

Later. She'll worry about that later. She sighs, looks back down at the list.

_Archangel_. She'll pick him up first.

* * *

She can't believe it.

_Garrus!_

Her heart leaps. He sits on the crates, his sniper rifle propped up on his turian toes, and regards her coolly.

"Shepard," he says, and his tone is guarded. "I thought you were dead."

"Garrus! What are you doing here?"

"Just keeping my skills sharp," he says, and he looks down, his eyes half closed, his voice soft, tired. "A little target practice."

_What's happened? _

Pain is written in Garrus' face. In the curve of his back. And the way he holds his gun like it's the only thing he has left in the world.

Guilt.

"Are you okay?" Her voice, gentle.

"Been better," he says, and looks up. His blue eyes fix on her. "But it sure is good to see a friendly face."

_I wish I'd been there for you._

And time…

freezes…

rewinds…

"Joker's still in the cockpit," Kaidan says, "He won't evacuate."

The Normandy is burning around her. Shepard pauses, extinguisher in hand. She looks towards the lifts, back to the escape pods. She tosses the extinguisher to Kaidan, pulls open the hatch, and fiddles with the circuits. The screen flickers back to life.

"We don't have time," she says, "We have to get to the shuttles."

Kaidan unleashes the last of the foam onto the fire, but it's still raging.

"We can't just leave him," he says. He throws the empty cylinder to the side, and starts to make for the stairs, but Shepard stands in his way. Stares him down.

"I gave you an order, Alenko. Get to the shuttles." He stands there for a few moments more, silent. Then turns, and runs toward the escape pods.

She follows.

_No, wait, I can't._

She watches out the window as the Normandy is destroyed, Joker along with it.

_No._

And time…

freezes…

rewinds…

"Joker, she's lost. And you are _not_ going down with the ship." She physically hauls him out of his chair, throws him over her shoulder.

"Hey!" he cries, but it is too late. She shoves him inside the escape pod, steps back to hit the release. "Wait, aren't you coming?" But she knows she won't be. She hits the button to eject the shuttle, and lets the explosion propel her into space.

_Again._

Time…

bends back…

And she's looking back at Garrus. At the pain written in the bend of his back and the grip on his gun.

"Been better," he says, and he looks up. His blue eyes fix on her. "But it sure is good to see a friendly face."

**END CHAPTER 2**

* * *

**Author's Note:** I'm on a roll with this story! Thank you to everyone who has reviewed, it helps to keep me going. :D


	3. Dreams

**Chapter 3: Dreams**

"I can't control it," says Kelly, exasperation in her voice. "EDI, can you do anything?"

"The parameters you set for the simulation do not allow me to interfere," comes the calm voice of the Artificial Intelligence.

"Goddamnit, EDI, can't you change the parameters?"

"The parameters do not let me."

Kelly throws her hands up in the air, and lets out an exasperated cry.

"Maybe we should let her continue," Chakwas says, her eyes not leaving the screen. "She seems to be working things out on her own."

"Working things out? How?" Kelly comes over and stands beside her.

"She almost changed the timeline again, and let Joker die. But she didn't."

"Kaidan's still alive, though. I don't think she's going to let him die."

"I think we should just watch, see what she does."

"Miranda is going to _kill_ me."

"I'll handle Miranda. Let's just wait and see."

* * *

When Shepard sees Kaidan on the colony of Horizon, she wonders why she didn't think of him before now. Why she didn't try to contact him.

_I thought he was dead._

But now it is very obvious that he is not. And she has no idea why she thought he was.

"Commander Shepard," Kaidan says, walking out from behind the buildings. "Captain of the Normandy. The first human Spectre. Saviour of the Citadel." His voice is loving. Her heart leaps. "I thought you were dead, Shepard. We all did."

And then he is standing right in front of her. _Commander Alenko now_, she reminds herself.

For a moment, they face each other, not sure what to do. And then he steps forward, embraces her, and she could cry.

Garrus watches, his face unreadable.

"It's been too long, Kaidan. How have you been?"

"Is that all you have to say?" he lets out a frustrated breath. "You show up after _two years_, and just act like nothing has happened?"

"Kaidan, I…" but how can she explain? _I thought you were dead. You thought I was dead. Mistakes happen, let's laugh about it, have some beers?_

"I thought we had something, Shepard. Something real." His voice is angry. "I loved you." He steps away from her, crosses his arms. "Thinking you were dead tore me apart. How could you put me through that? Why didn't you try to contact me? Why didn't you let me know you were alive?"

_I don't know_, she thinks, but her thoughts are confused, broken. Like this has happened a million times. Like it has never happened at all. She puts her hand to her forehead, massages her temples.

"I don't know," she says, and her voice sounds weak, "I _was_ dead. I thought you might be, too… I had a dream you were."

He shakes his head.

"That's not good enough, Shepard. You had a dream I was dead? What kind of crap is that? Well, you know what, I moved on. But then I got reports of you and Cerberus. Cerberus!"

"The Alliance turned their back when I told them about the Reaper threat. Cerberus is the only one who believed me, who backed me."

"You can't really believe that! We both know what Cerberus is like. What they're capable of. I wanted to believe the rumours that you were alive, but I never expected _anything _like this. You turned your back on everything we believed in. You betrayed the Alliance. You betrayed _me_."

"Kaidan, you know me, you know I'd only do this for the right reasons."

"I don't know anything anymore," says Kaidan, unfolding his arms and turning away. "And I certainly don't know you."

"Dammit, Kaidan," Garrus broke in from behind her. "You're so focused on Cerberus, you can't see what's right in front of you. _Who_ is right in front of you. This is _Shepard_, pull yourself together!"

Shepard glances back at Garrus, who looks as angry as Kaidan, then back to the man in front of her.

"Kaidan," she says, changing the tone of her voice, "Come with me. I could use someone like you in my crew. It'll be just like old times. And that way you can keep an eye on Cerberus, and me."

Kaidan turns back, crosses his arms again. He's silent for a long moment, and then he says,

"I'll think about it. I'm not as free as you to move around. I'll need some time. But… maybe." He begins to walk away, and then calls back over his shoulder, "_Someone_ has to keep Cerberus honest."

"Well that went better than it might have," says Garrus after Kaidan is gone, and Shepard turns back to face him.

"Thank you," she says. "For saying that. I think… I think you might have helped change his mind."

Garrus shrugs, no mean feat in his heavy armour.

"He's an idiot if he walks away from you," he says. "_Someone_ needed to remind him of that."

* * *

"She's replayed what happened with Williams," Kelly says. She takes a sip of the hot coffee from the dispensing machine. "Except she thinks that if it had been Kaidan, he would have understood."

"I don't know if he would have," Chakwas says, adds a spoonful of sugar to her cup, and stirs. "His first loyalty was always to the Alliance."

"Well, that's not how she imagines him," says Kelly.

The doors to the med bay slide open, and a grim-faced turian enters, stalking towards Shepard's gurney.

"Wait-" Kelly says, at the same time that Chakwas says, "Garrus!"

"I heard about Shepard," he says, his two-toned voice rumbling in his chest. He makes his way to her side and looks down at her. "How long has she been under?"

"It's a little more complicated than that," says Kelly, a the same time that Chakwas says, "We need to talk."

Garrus blinks, looks at the two females, then back down at the Commander. He takes her hand, and gently entwines his talons with her fingers. "Then talk," he says, and his tone will accept nothing else.

"I don't like it," Garrus says once they are through. "You're basically spying on her."

"Miranda authorised it," says Kelly, at the same time that Chakwas says,

"It seems to be working. She's revisiting everything that hurt her."

"Everything?" Garrus asks, and there is a slight catch in his voice.

"You might not want to see this," Kelly says. "You should probably wait until she's awake-"

"I'm not going anywhere," Garrus says. And Chakwas abruptly remembers how Shepard refused to leave his side when he was on the same gurney, half his face destroyed by a gunship.

Kelly is about to object, but Chakwas gently puts a hand on her forearm. "He can stay," she says, and Garrus rumbles in agreement.

* * *

It's a surprise when Kaidan turns up on the Citadel, bags packed. He catches Shepard's expression, says "You offered me a chance to keep Cerberus honest. I'm taking you up on it." Then he's walking past her, towards the crew's sleeping pods.

_I guess it's too much to hope for, that he'd go to my quarters._

But it's a start.

**END CHAPTER 3**

* * *

**Author's Note:** Thank you everyone for your encouragement, and interest in this story! I'm looking forward to seeing where this goes as much as you are - I hope that you'll stay along for the ride! :D


	4. Unwelcome Truths

**Chapter 4: Unwelcome Truths**

"This has gone totally pear-shaped," says Kelly. "Kaidan is not supposed to be alive, and he is _definitely_ not supposed to be on the Normandy. I'm terminating the program, we have no choice."

"Wait-" And it's both Garrus and Chakwas at once.

Kelly turns towards him. "Do you really want to watch this?" she asks. "She clearly still has feelings for Kaidan."

Chakwas turns toward him to catch his reaction. Garrus shifts awkwardly under their combined scrutiny.

"I have to know," he says eventually, his voice soft. "I have to know whether she's with me because of me or… because Kaidan isn't around. This could let me know, for sure."

"Garrus," the Doctor says gently, "You may not want to know the answer."

"Knowing is better than not knowing. I'm not saying it would ruin things with Shepard. I just need to know."

Chakwas and Kelly exchange looks. Garrus remains stoic, no expression showing on his features.

"I don't know," says Chakwas. "You have a personal interest in the Commander. I'm not sure it's right."

But Kelly is looking at the stoic turian with soft, watery eyes.

"I think we can let him stay," she says. "It's not like he can control what she sees." She turns to the turian, "But I'm warning you-"

"I know, I know. It's my fault if I get hurt."

Kelly and Chakwas exchange looks again, and Chakwas shrugs. "Alright then."

* * *

When she walks into the Comms room, Kaidan and Miranda are facing each other off across the table. He's jabbing a finger into his gloved palm, classic Kaidan for "I've got a problem and I'm damn well going to let you know about it." Miranda looks calmer, but her arms are folded across her chest defensively. When Shepard walks in Miranda turns towards her, relief evident on her face.

"Captain, please explain to Commander Alenko why we need to investigate the Collector Ship. He's convinced that it's all a plot masterminded by the Illusive Man."

Kaidan also turns to her. "Just think about it, Commander. The last time we met one of these, you _died_ and the Normandy was destroyed. How was one turian patrol ship able to take it out?"

Shepard looks from Miranda to Kaidan. _Should've figured these two hot-heads would clash._ Both of them are looking at her like she'll take their side. She shifts her weight from one foot to the other, then clasps her hands behind her back.

"It's possible the ship was damaged by the GARDIAN towers you installed on Horizon, making it a soft target," she says.

"There's nothing about the Collectors you could call soft." Kaidan folds his arms, his brows lowering over his eyes. "I don't like it, Shepard. How do you know the information is good?"

"The Illusive Man spent billions of dollars bringing Shepard back," says Miranda, rolling her eyes, "I spent two years of mylife. Do you really think either of us would send her into danger unnecessarily?"

Kaidan eyes Shepard's executive officer, arms still crossed, then rolls his shoulders and gives a small, noncommittal grunt.

Miranda turns back to Shepard, her eyes flashing triumph. "Joker has the coordinates, we're ready to go whenever you are."

Miranda walks out of the room, a subtle bounce in her step, and Shepard and Kaidan are left alone.

Kaidan looks at her, eyes hard, then turns to leave as well. Shepard catches his arm, and he turns back, eyebrow raised expectantly.

"Are we going to have a problem, Alenko?" she asks quietly.

"No, ma'am."

"Miranda is my XO, and a damn fine one at that. I won't have you, or anyone, questioning her orders."

Kaidan nods, but there's a riposte hiding behind clenched teeth.

"Out with it, soldier."

He stands straighter, his back stiff. "She's Cerberus, ma'am. She can't be trusted."

"And what about me? Can I be trusted?"

What should have been – what once would have been – an easy answer, is not forthcoming. He's silent for a long moment, then says-

"That's what I'm here to decide."

It stings, but it's not unexpected. She nods.

"Okay Commander. In the meantime, I'm running this vessel like an Alliance ship and you will obey my orders and those of my officers."

"Understood, ma'am." He salutes and leaves the room.

* * *

The situation isn't helped when the Collector ship turns out to be a trap. One the Illusive Man knew about.

In the privacy of the Comms room, with only her and the Illusive Man as witnesses, the frustration and rage leaks out.

"You betrayed us, just like I knew you would. I can't trust you." _Are those her words? Or Kaidan's?_

The Illusive Man calmly takes a drag on his cigarette, and looks at the glowing tip while he speaks. "We're at war, Shepard. Yes, it was a trap, but I was confident in your abilities."

"You could have told me the plan." _So I didn't tell Kaidan that we could trust you._

"I needed the Collectors to believe they had the upper hand. Besides, I wouldn't have sent you in if I didn't think you would succeed."

"And what about my crew? What am I going to tell them?" _What am I going to tell Kaidan?_

"Sometimes these decisions have to be made. I suggest you tell your crew I didn't risk their lives unnecessarily. It will make things… easier, going forward.

Kaidan is there when she relays the news to the crew, and Shepard's eyes slide over to him, but he tactfully says nothing, even when Jacob accuses the Illusive Man of selling them out. She looks away to find Miranda looking at her, eyes filled with – worry?

Mordin speaks up, "He lied to us. Used us. Needed access to the Collector data banks. Necessary risk."

"There really wasn't any other choice," Shepard says, and she can feel Kaidan's eyes on her.

* * *

Kaidan storms in and starts speaking, even before she asks him to enter.

"So we're going to investigate a derelict reaper now? We didn't have enough betrayal on the Collector ship?"

Shepard is sitting on the couch, a book open on her lap, and watches as Kaidan walks in, slowly comes to a stop, and looks around. "Wow, they sure upgraded your digs."

Shepard slips the bookmark into her page, closes it, and puts it down on the coffee table. "Is there something I can do for you, Commander Alenko?"

"Yes, there is," he says, and walks down the steps to stand in front of her. "You call tell me what in the galaxy is going through your head to trust this guy after he's already betrayed us once."

"You have to admit, it paid off. And I already explained that he couldn't tell us without tipping off the Collectors."

"You buy that crap? He could feed you any lie, and you'd chomp it right down."

Shepard is silent a moment, feeling her hackles rise, then it spills out. "You think the Alliance brass is any better? Remember that first "shakedown run"? We didn't get told what it was for until _after_ we received the distress call. And, dammit, they don't want to believe the Reapers are a threat even after one landed in the middle of the goddamned Citadel. The Illusive Man does what he has to, to give us the best chance of defeating them."

"I can't believe you're sitting here defending him, the head of Cerberus. The dog himself. You've changed, Shepard, and I'm not sure I like it at all."

She stands, and takes a step forward.

"I've changed? What about you? You used to believe in things, once. You used to believe in me. Now you're just a lapdog for the Alliance. Remember when we mutinied, took the Normandy? You were with me then. Now, well, I guess they bought you with that shiny medal of yours."

"Goddammit, Shepard. I'm here, aren't I? You think they'd be happy if they found out?"

"Who knows, you might have been sent as a fracking spy for all I know. The Alliance isn't above that."

"I'm here because I want to be. You should know me well enough to know that."

They stop just in front of each other, breathing heavily. Then Kaidan turns on his heel, and Shepard can hear the quiet _swoosh_ of the door as he leaves. She stands there a few moments more, glances at her book, and crosses to the bed, flopping down on it with her palms over her eyes.

* * *

**Author's Note:** I'm back after finishing Dragon Age 2! There's 2-3 chapters left of this story... things are starting to get moving! Thanks everyone for your favourites and reviews, you help to keep me going!


	5. Reprieve

**Chapter 5: Reprieve**

When the door to the main battery slides open, the turian's back is facing her. His talons fly across the console, even though it was designed for human hands, and it is magic to watch him for a moment.

"Shepard," he says over his shoulder, "I'll be with you in just a minute. I'm finishing the last of these calibrations."

"How did you know it was me?" she asks, crosses to the crate near the wall, and takes a seat.

"Easy," he says, "No one else visits me."

He continues working on the console for a few moments more, and then he turns around, looking satisfied with himself.

"How's she running?" she asks.

"Fast and tight, she's a beautiful gun."

"I'm glad we had her installed. The Collectors won't know what hit them."

She receives a toothy grin in response, as much malice as it is glee.

"I can't wait. But you didn't come here to talk about guns," he says, "What's up?"

She thinks about dodging the question, but his blue eyes are on her and, well, this is _Garrus_. One of her oldest friends, and one of the few people on board who _aren't_ Cerberus. If she can trust anyone, it's him.

He's still looking at her.

"Have I changed?" she asks, brow furrowed. "You know, since I died?"

Garrus tilts his head to the side, and with one talon he distractedly taps the glass of the console next to him.

"Dying would change anyone," he says after a moment. "Considering the circumstances, you've hardly changed at all."

"But I have changed. How?"

Garrus closes his eyes for a moment, then opens them again and looks right at her. "You're a little harder than you used to be," he says, "A little more distant. Although I don't know how much that has to do with you, and how much it has to do with the fact that we're stuck on a ship full of Cerberus officers."

"Is that all?"

Garrus narrows his eyes. "You're more cynical. I don't think you trust the Alliance as much, or the Citadel."

"It's hard to trust anyone when they refuse to see what's right in front of them because it's too _inconvenient_."

Garrus holds up his hands, a disarming gesture, "Hey, I'm on your side, Shepard. It's why I left C-Sec."

Shepard looks down at her clasped hands. _Kaidan was right – I have changed. Maybe too much._

Garrus's voice interrupts her thoughts. "What is this about, Shepard?" His voice gentles, "Are things not going well with Alenko? Because I think-"

She stands abruptly, cutting him off. "Things are fine between the Commander and I," she says. "He's here to keep Cerberus on the straight and narrow, and that's what he's doing. Maybe it'll win us some points with the Alliance again." She pauses near the doorway, turning back to say, "Thanks for the talk, Garrus," and then she is gone.

* * *

She's in the Mess, shovelling reconstituted mashed potato onto her plate, when Kaidan slides up beside her holding his tray. He doesn't say anything, so Shepard moves onto the peas.

"I'm sorry about what I said," he says, talking in the direction of the mashed potato. They move along down the line, and Shepard grabs a ladle of stew. He starts on the peas. "I shouldn't have questioned your judgement. Or your loyalties."

"Apology accepted," she says, scooping a second ladleful of stew. With Gardner's new ingredients, it smells divine.

Kaidan follows her over to the table and puts his tray down opposite hers. "I just don't understand why you didn't contact me first. Don't you know what you dying did to me?"

"Not as much as it did to me," she says around a mouthful of potato and peas. She swallows. "Look, Kaidan, I woke up inside a Cerberus facility and that was the first thing I knew. It took a long time to sink in that I'd been dead for two years. I haven't been thinking entirely straight. I was convinced that you died back on Virmire instead of Ashley. Maybe I dreamt that while I was gone, I don't know."

Kaidan chews a piece of meat thoughtfully. "You really thought I was dead?"

"I'm not lying to you."

"Okay, say I buy it. It makes more sense then, what you're doing. But- doesn't it concern you at all that this team you're putting together are all outlaws of one type or another?"

"There was a time when _we _were deserters," she says. "Because of something we believed in."

"That was different."

"Is it?"

"We believed in that mission. These people you're pulling together are coming from everywhere. A tank-grown Krogan, a Justicar, an assassin for Christ's sake. What do they care about Reapers?"

"They realise how big the threat is, which is more than the Alliance or the Council has done. They might not play by the rules all the time, but they know how to make things happen. If there's one thing I've learnt, it's that sometimes you have to go outside the system."

"You're sounding more and more like Cerberus, Shepard. We could convince the Council to see the threat. Maybe if I go with you, add my voice to yours."

"They won't think you've been corrupted by Cerberus too?"

That causes an uneasy silence, and Shepard takes the opportunity to press more mashed potato into her mouth.

"We both know the Council isn't interested," Shepard says around her mouthful. "Playing by the rules didn't work last time, and it's not going to work this time. I need people who are willing to take risks. People who are willing to believe."

"You could have given me a chance, Shepard. We could have built a real team."

"This is a real team, Kaidan. This is _my_ team. And I won't have you bad mouthing them, not to me or anyone else."

He sighs heavily, puts his spoon down on the side of his plate. "You're right, I'm sorry. It's just… so much has changed. God, even Garrus has changed… and Tali, too. Two years is a long time."

"I know," she says, and her voice is gentler. "God, I know. And what's worse is, for me it feels like it's only been a few months."

Kaidan pauses, his fork in mid-air. He leans forward, dark eyes on her. "I'm sorry, Shepard. I hadn't thought about how it must be for you."

* * *

Chakwas is only half watching the screen. With her other eye, she's watching the turian standing next to the bed, and the way his talons have tightened on Shepard's hand. His mandibles are tight against his jaw, and she can see tension in his muscles.

"You don't have to stay here," she says gently, and Garrus whips his gaze from the monitor to look straight at her.

"He doesn't deserve a second chance," he growls, and his gaze drops to Shepard's peaceful face, as though willing her to listen. "He wasn't there for you, didn't even _think_ of how you felt."

Kelly reaches out, gently touches the back of Garrus's hand, and he jerks it away, as though burned.

"Garrus," she says, "You don't have to watch this."

"No, I have to stay. I have to know. I want to see it through."

Chakwas looks over to Kelly.

"None of this is real, Garrus. Kaidan's not real, the-"

"Shepard's real," he says grimly. "Her feelings are real. And that's what's important."

"You're not going to get him to leave," says Chakwas, and turns her attention back to the screen.

* * *

Garrus is working on the guns when the door slides open. He turns as Shepard enters.

"Kelly said you wanted to speak to me," she says, standing in the doorway, and he nods,

"I'm glad you came by. I've got something, and I need your help. You remember Sidonis? The one who betrayed my team? I've found a lead on him."

* * *

**Author's Note:** Gah! Sorry for how long it's been since my last update, another plot bunny had me by the ears and wouldn't let me go. Not too long to go for this story! Thanks everyone who has stayed along for the ride! :)


	6. Consequence

**Chapter 6: Consequence**

Garrus and Kaidan are silent in the skycar on the way to Orbital Lounge. When Garrus pulls the car up, he sits there for a moment, unmoving.

"Harkin's a bloody menace," he says. "We shouldn't have just let him go, he deserves to be punished."

Shepard looks over at him. He's facing out the window, his mandibles pulled tight against his jaw. "I'm getting a little worried about you Garrus," she says, "You were pretty hard on Harkin."

"You don't think he deserved it?" He turns to look at her.

"It's just not like you." Under his intense scrutiny, she look out the window at the lights of the Citadel and, after a moment, Garrus also turns away.

"What do you want from me, Shepard? What would _you_ do if someone betrayed you?"

She thinks of Kaidan, and everything that's happened.

_But none of it is even remotely the same as this._

"I don't know," she says honestly. "But I wouldn't let it change me."

She turns to Garrus, and he also turns to face her. In the tight confines of the car, she feels it's just him and her, pressed close. She looks into his eyes: blue steel. _And pain._

"It's not too late," she says, almost a whisper. "You don't have to go through with this."

"Who's going to bring Sidonis to justice if I don't? Nobody else knows what he's done, nobody else cares." He pauses, closes his eyes, squeezes them tightly. "I don't see any other options. He deserves to die." His voice is resigned, not angry.

"I understand what you're going through," she says, "but do you really want to kill him?"

"I appreciate your concern…" he says, opens his eyes, looks straight at her. "But I'm not you."

_No, he's not. And you're not who you used to be, either._

It's clear that Garrus needs this. Shepard is silent. Swallows. Nods. Then, quietly, "What do you need me to do?"

Garrus' eyes soften, though his voice is still gruff, "Keep him talking, and don't get in my way. I'll let you know when he's in my sights."

When Garrus leaves the car, Kaidan leans forward from the back seat. "You aren't really going to let him do this, are you?"

"It's his choice, Kaidan. He's the one who's going to have to live with it."

"So you're just going to wash your hands of it?"

"No. I'm going to respect his choice."

"And what of Sidonis?"

"He already chose. And he's about to learn that actions have consequences."

She opens the door and steps out of the car.

"I can't believe you're doing this," Kaidan says as the door swings shut behind her.

* * *

Chakwas and Kelly are looking straight at Garrus, who seems reluctant to meet their gaze.

"Did that really happen?" Kelly asks and then, without receiving a reply, "She never told me."

"It wasn't hers to tell," Garrus says, voice sounding like it's sinking even deeper into his chest. "Kaidan and his moralising weren't there, of course."

"But… she helped you kill Sidonis?" Chakwas asks.

"Yes." He says it reluctantly, the words dragged from him.

"Wow," Kelly says, and they are all silent.

"That's very unlike Shepard," Chakwas says, glancing over at her.

"I appreciate what she did for me," says Garrus, "the sacrifice she made. It meant- it _means_ a lot to me."

"So did it work? Killing Sidonis, I mean."

"Oh yes," says Garrus, and glances over at the flame-haired woman. "It did." And then he smiles.

* * *

"Okay Shepard, I'm set up. Can you hear me?" Garrus' voice came over her speaker.

"Loud and clear." She scans the orbital lounge.

"There he is. On the bench. Wave him over, and keep him talking."

She spots Sidonis, walks over to him, and identifies herself as one of Fade's operatives. At that moment, Kaidan's voice comes over her headset.

"Shepard, you don't have to do this. Warn Sidonis, get him out of there. We can bring him to justice, properly."

She glances to the side. Kaidan is stepping out of a cab. He sees her, and starts towards them.

"So, what's this about?" Sidonis asks, his eyes shifting from side to side. "What's going on?"

Garrus's voice in her ear: "You're in my shot, Shepard. Move to the side."

"Your identity's been compromised, Sidonis," she hears herself saying. "We need to move you to a safe location."

"Hey, don't say that name aloud. Ever."

"Shepard, I'm telling you, this isn't justice. Not for you, not for Garrus, and definitely not for Sidonis."

"Just a few more seconds, Shepard. Keep him talking for just a few more seconds."

"Well, let's get this over with then," says Sidonis. He's starting to look nervous. "Are you one of Harkin's men? I don't remember seeing you before."

"That's it, Shepard. I'm ready. Step out of the way."

"Stay there, Shepard. I'm almost there."

She looks at the turian in front of her, whose mandibles have started to vibrate with ill-concealed stress. She can hear running footsteps behind her. And behind them, behind all of them, she knows there's a turian with a broken heart and a loaded gun.

_For you, Garrus. For everything I failed to do for you._

She steps aside.

"No!" Kaidan's voice.

And time…

freezes…

rewinds…

She's looking at the turian in front of her, whose mandibles have started to vibrate with ill-concealed stress. She can hear running footsteps behind her. And behind them, behind all of them, she knows there's a turian with a broken heart and a loaded gun.

_For you, Garrus. For everything I failed to do for you_.

She steps aside.

"No!" Kaidan's voice.

And time…

freezes…

rewinds…

She's looking at the turian in front of her, whose mandibles have started to vibrate with ill-concealed stress. _Not again_. She can hear running footsteps behind her. _Kaidan_. And behind him, behind all of them, she knows there's a turian with a broken heart and a loaded gun. _Garrus._

She has to make a decision._ Step aside, and prove everything that she has become, or turn him in and show that she's the same Shepard she once was._

The footsteps are getting closer.

But there's only one decision.

She steps aside.

"No!" Kaidan's voice. Then a shot rings out, and the turian in front of her is falling to his knees, a shocked expression on his face. And Kaidan's hand is on her shoulder, spinning her around to face him.

"Why did you do that?" he yells.

Shepard glances at the turian's corpse. Back to Kaidan.

"We'd better get out of here," she says, and her voice is thick.

_Shock_, the sensible part of her says.

Kaidan is still yelling at her, but it makes no sense. She walks past him, back towards the car.

Garrus meets her there, sniper rifle folded and replaced on his back. He meets her eyes, nods. This is not a time for words. And when the other Commander catches up to them he doesn't say anything either but his face is dark.

And no words are spoken all the way back to the Normandy.

* * *

"Shepard," says Garrus, stepping into her cabin. He looks around, and it strikes Shepard that this is the first time he's been in here. He has a bottle of wine in his hand. "I just wanted to say thank you."

Shepard glances over from where she sits at her desk, filing her report on the incident. Miranda had surprisingly approved, saying that the Collector mission took precedence over all else… and that she should do whatever is necessary to win the total commitment of her team. From the way Garrus is looking at her, it seems it succeeded.

She stands up, smiles, though it still feels slightly broken. "That's okay, Garrus. I'm glad I was there for you."

Garrus looks awkward holding the wine. He puts it down on the nearest shelf, next to her hamster, which he looks curiously at for a second. Then his eyes turn to her, and then away. "I know that it caused some… problems between you and Commander Alenko," he says.

"None that didn't already exist," she says. "He was already questioning my loyalties. This has just confirmed his suspicions."

Garrus looks up at her, eyes twinkling. "Neither of us have been very good at playing by the rules," he says.

"No," she agrees, and this time the smile is genuine. And, from somewhere, she knows that this moment somehow feels right. Like things are sliding back into place.

Garrus inches forward slightly and, with only a little hesitation, reaches out to gently touch the side of her arm with his hand.

"I like that about you," he says. Shepard's gaze travels from his hand, up his arm, to his eyes. He's looking at her, unflinching. Blue steel, but no pain. Something else is glowing within his eyes, and she's surprised to feel a mirroring warmth flare into existence.

"I like that about you too," she says, and he nods slightly and seems to stand straighter, like a weight has been lifted from his shoulders.

"I should return to my station," he says. "But- if you're needing someone to share the wine with…" he pauses, "You know where I am." Then he salutes, says "Shepard," and leaves the cabin.

Shepard returns to her paperwork, feeling strangely giddy, but it isn't long before another chime at the door interrupts her.

"Shepard." Kaidan is standing in the doorway, a rucksack slung over his shoulder. Shepard doesn't step back to let him in, and he doesn't try to move forward. "I just wanted to tell you I'm leaving."

"I understand," she says. It's a massive breach of protocol, but it's for the best, so Shepard lets its slide. Kaidan shifts his weight from one foot to the other, and Shepard raises an eyebrow.

"I'd hoped things would be different," he says, and Shepard shakes her head.

"No, you hoped they would be exactly the same," she says. "We've changed. Both of us."

"I know. And, for what it's worth, I'm sorry."

"Don't be sorry, Kaidan. There's nothing to be sorry about."

He nods. "I won't cause any trouble for you," he says after a moment. "Just so you know."

"I know," she says, and smiles. "You haven't changed _that_ much."

He doesn't mirror her smile. "Maybe… maybe if all this hadn't happened, we could've been something."

"Maybe," she says, but her heart is still beating its giddy patter for a shy turian with blue eyes and a bottle of wine.

Maybe he reads it in her tone, or her stance, because she can see it hit him. "Well, I'll see you around, Shepard."

"Goodbye, Kaidan."

And then he is gone.

* * *

**Author's Note:** Thanks everyone for sticking around for this story, it took me awhile to get the latest chapter up - I'm taking the time to make sure I get it right. :D Reviews and comments are welcome, there's one more chapter to go after this one!


	7. Completion

**Epilogue: Completion**

He comes to her the night before the Omega 4 relay. He's nervous, and shy, but his eyes are burning with blue flame. Her hand floats up to caress his scar.

She doesn't know what this is. She doesn't know what the morning will bring. But right here, right now, she knows it's what she wants.

It is only later, much later, that she thinks of Kaidan.

Walking out of the shower, towelling her hair, she glances at her desk, at the drawer where she stashed his photo. Sliding it open, she looks down at his impassive face, and wonders what he is doing now, a million miles and a thousand worlds away.

_Probably much the same as me_, she thinks wryly. _He was never one for suffering without company._ She wonders, for a moment, whether that hurts.

But then Garrus calls her. And she slides the drawer closed.

* * *

When she wakes, Garrus is lying beside her, his talons entangled with her fingers. She sighs happily, and moves to roll over, but her fingers touch cold metal and her eyes fly open. She is in the Med Bay, the two of them crammed together on a single gurney. Chakwas is asleep slumped over her desk. There are all manner of machines hooked up to her, but when she flexes her arms and legs she can feel no injury.

Slowly, it comes flooding back.

The mission. Their success. Feeling empty, useless, finally without a driving purpose. Then – turning her gun on Chakwas. _Convinced_ that she was a Cerberus spy.

Guilt lays heavy on her heart.

The door opens, and she turns her head, but finds wires in her way. She's peeling the pads out from under her hair as Miranda walks in.

"Shepard," she says, and stops in the middle of the room, folding her arms. "It's good to see you awake."

"What did you do?"

"What do you remember?" The XO asks cautiously.

"I remember what happened. But I don't know why I'm hooked up to these machines."

"Consider it therapy. You've been closely monitored, and I understand that your recovery should now be complete."

"You authorised this?"

Miranda nods.

Shepard pulls the last of the electrodes from her scalp, drops them onto the gurney, careful not to disturb Garrus.

"Then thank you."

"I'm glad to see you back to your old self. You had us worried there for awhile."

"I've seen it before. I never thought it would be me."

Miranda says nothing, and Chakwas makes a small noise and slowly lifts her head.

"Shepard?"

"Doctor Chakwas." Shepard nods in her direction.

"So it worked?" The doctor pushes back her chair and slowly stands up.

"Don't sound so surprised, doctor."

"I'm- just glad." There's a small hitch to her voice.

"I need to apologise-" Shepard starts.

"No," Chakwas holds up her hand, cutting her off. "You don't need to apologise. We do. You've carried the weight of this entire mission, and never complained. None of us did anywhere near enough to help you."

"Doctor, this is my duty. As a Spectre. As a soldier. As someone who knows the truth about the Reaper threat."

"But we're with you, Shepard." That's Garrus' two-toned voice, and he's sitting up on the gurney. He stands up. "You can rely on us."

"Vakarian is right, Commander. This is your crew."

Shepherd looks from Chakwas, to Garrus, to Miranda. There's nothing but trust in their eyes. She swallows down a hard lump forming in her chest, nods, and turns to the Doctor.

"So am I fit for duty, Doctor?"

"I'd like to run a few tests, but my guess is that you'll be back on deck in a couple of days."

"Good." She looks at these three again, and there is only gratitude. For forgiving failure. For trusting her despite it. And, for the first time, she thinks that maybe – just maybe – they have a chance against what's coming.

* * *

She sits down at her desk, spins the terminal to face her. Then, on a whim, opens the drawer next to her. Lying face up on the bottom of the drawer is the photo of Kaidan. She remembers when she could finally take it off her desk without feeling like she was betraying him all over again.

_Kaidan_.

In her dream, he was alive. She wishes that he was still, but somehow it lacks the intensity it once used to have.

She looks at the photo for a moment more, then slides the drawer closed. And uses the terminal to call Garrus up to her quarters.

**END**

* * *

**Author's Note:** Thanks everyone for sticking with me, and waiting so long for the final chapter! This is just a short one, wrapping up a few loose ends. I've enjoyed this story, and I hope you have too!


End file.

Mass Effect, Angst, Romance